At a Glance

Why Get Tested?

To determine whether you have an infection of your digestive tract due to the presence of disease-causing (pathogenic) bacteria

When to Get Tested?

When you have diarrhea, abdominal cramps, with or without fever, lasting more than a few days

Sample Required?

A fresh stool sample or one that has been placed in a transport medium (a collection vial containing a preservative)

Test Preparation Needed?

None

The Test Sample

What is being tested?

The stool culture is a test that detects and identifies bacteria that cause infections of the lower digestive tract. The test distinguishes between the types of bacteria that cause disease (pathogenic) and the types that are normally found in the digestive tract (normal flora). The test helps to determine if pathogenic bacteria are the cause of gastrointestinal symptoms (gastroenteritis).

The bacteria found in stool are representative of the bacteria that are present in the gastrointestinal tract. Certain bacteria and fungi called normal flora inhabit everyone's gastrointestinal tract. They play an important role in the digestion of food, and their presence keeps a check on the growth of disease-causing bacteria. Sometimes, the balance of the normal flora may be affected by the administration of broad-spectrum antibiotics; the drugs inhibit the growth of normal flora and allow bacteria resistant to the antibiotic to survive and overgrow the digestive tract. The normal flora may also be affected by anti-cancer drugs and when a person has a weakened immune system, leading to bacterial overgrowth and symptoms such as diarrhea and abdominal pain.

Pathogenic bacteria can enter and infect the digestive tract when someone eats food or drinks water that is contaminated. Examples of contaminated sources include raw or undercooked eggs, poultry or beef, unpasteurized milk, and untreated water from lakes, streams, and (occasionally) from community water supplies.

People who travel outside the U.S., especially to developing nations, may face a greater risk of being exposed to disease-causing bacteria. Some of these bacteria may be true pathogens while others are strains of gastrointestinal bacteria that are normal flora for the local inhabitants but cause gastrointestinal distress to the tourist. Visitors may become infected by eating or drinking anything that has been contaminated with the bacteria, even things as simple as tap water, ice cubes in a drink, a fresh salad, or food from a vendor's stall.

The most common symptoms of a pathogenic bacterial infection are prolonged diarrhea, bloody diarrhea, mucus in the stool, abdominal pain and cramping, and nausea. If diarrhea lasts more than a few days, it may lead to complications such as dehydration and electrolyte imbalance - dangerous conditions, especially in children and the elderly. Dehydration can cause symptoms such as dry skin, fatigue, and light-headedness.

Severely affected people may require hospitalization to replace lost fluids and electrolytes. Hemolytic uremic syndrome is a serious complication characterized by the destruction of red blood cells and kidney failure that may occasionally arise from an infection with a toxin-producing strain of the bacteria Escherichia coli. The condition is most frequently seen in children, the elderly, and those with weakened immune systems.

Some of the most common pathogenic bacteria that cause infections in the U.S. and their most frequently encountered sources include:

Salmonella - found in raw eggs (even intact disinfected eggs), raw poultry uncooked vegetables, and in reptiles; pets, such as lizards and turtles, may carry salmonella in their intestines without being ill themselves. Some humans may become carriers of salmonella. Salmonella may be transmitted person-to-person.

Shigella - found in food and water contaminated with stool, and from infected-person to person when careful sanitation is not observed; for instance, it can be a challenge to prevent the spread of Shigella within a family and in a daycare or nursing home setting since even a very few organisms may cause disease.

Campylobacter - found in raw or undercooked poultry; it is the most common cause of bacterial diarrhea in the U.S. It may become especially serious if it spreads to the bloodstream, and it occasionally causes long-term complications such as arthritis and Guillain-Barré syndrome.

Escherichia coli 0157:H7 and other toxin-producing E. coli (most strains of E. coli are considered normal flora and do not cause disease) - found in raw or undercooked hamburger/beef, spinach, or unpasteurized cider; causes bloody diarrhea and may lead to hemolytic uremic syndrome.

Clostridium difficile - may be present as part of the normal flora, but use of broad-spectrum antibiotics can result in an overgrowth of these bacteria. Toxin-producing strains can cause diarrhea and other serious complications.

A wide variety of other bacteria may sometimes cause diarrhea. These may include: Aeromonas species, Staphylococcus aureus, Yersinia enterocolitica, Vibrio cholerae and other Vibrio species.

How is the sample collected for testing?

A fresh stool sample is collected in a sterile container. The stool sample should not be contaminated with urine or water. Once it has been collected, the stool should be taken to the laboratory within about an hour after collection or should be transferred into a vial containing a preservative and taken to the lab as soon as possible. For infants, a stool sample is usually collected with a swab of the rectum.

Is any test preparation needed to ensure the quality of the sample?

The Test

How is it used?

A stool culture is used to detect the presence of disease-causing bacteria (pathogenic) and help diagnose an infection of the digestive tract. It is often used along with other tests such as an O&P test that detects parasites in the stool and/or Clostridium difficile and C. difficile toxin tests, to help determine the cause of prolonged diarrhea. In establishing the cause, the test can help guide treatment, determining whether antibiotics or other medication may be necessary to resolve symptoms.

When is it ordered?

Stool cultures may be ordered when someone has signs and symptoms of an infection of the digestive tract. This is especially true when the affected person has eaten food or drunk fluids that the doctor suspect may have been contaminated with pathogenicbacteria, such as undercooked meat or raw eggs, or the same food that has made others ill. Recent travel outside the United States may also suggest possible food contamination. Some signs and symptoms of infection include:

Diarrhea that lasts more than a few days and may contain blood and/or mucus

Abdominal pain and cramping

Nausea, vomiting

Fever

Not everyone who has these symptoms will necessarily have testing done or be treated with antibiotics. In people who have healthy immune systems, these infections often resolve with supportive care and without the use of antibiotics. However, if symptoms become severe or are present in an infant, a young child, an elderly person or someone with a weakened immune system, then testing and treatment are usually warranted.

A doctor may order one or more stool cultures when someone has had a previous pathogenic bacterial infection of the gastrointestinal tract and has either been treated for it or it has resolved on its own. This may be done to verify that the pathogenic bacteria are no longer detectable because in some cases people can become carriers of the bacteria. Carriers are not ill themselves, but they can infect other people.

What does the test result mean?

If a stool culture is positive for pathogenicbacteria, then they are the most likely cause of the diarrhea and other symptoms. Results are frequently reported out with the name of the pathogenic bacteria that was detected. Laboratories typically evaluate stool cultures for the most common intestinal pathogens:

Campylobacter species

Salmonella species

Shigella species

Depending on the affected person's medical and/or travel history, tests for other pathogens or potential pathogens may be included or be separately available. Some of these include:

Certain strains of Clostridium difficile can cause intestinal disease and diarrhea. If these strains are suspected to be the cause, then separate tests that detect the toxin-producing C. difficile will be performed.

Results of stool cultures that are reported as negative usually reflect the fact that the stool culture was checked for the most common pathogens at several intervals and none were found (not isolated). A report may state: "no Campylobacter isolated," "no Salmonella or Shigella isolated," etc. If the culture is negative for the major pathogens, then it is likely that the prolonged diarrhea is due to another cause or to a less common pathogen. It is also possible that pathogenic bacteria are present in the gastrointestinal tract, but there were too few bacteria in that particular stool sample to be detected. If a doctor suspects that this is the case and symptoms continue, he may order a stool culture on another sample and/or follow up with other tests.

Most diarrheal disease is caused by a single pathogen, but it is possible to have an infection with more than one.

Is there anything else I should know?

Severe pathogenic bacterial infections of the gastrointestinal tract and those causing complications may be treated with antibiotics, but many uncomplicated cases are best left untreated with antibiotics. Those with healthy immune systems will usually get better on their own within a week or so. People are instructed in how to prevent the spread of the infection and are treated and monitored for symptoms such as dehydration.

Pathogenic bacterial infections are monitored on a community and sometimes national level. Other than foreign travel-related cases, health officials try to determine where an infection came from so that they can address any potential public health concerns. Bacterial isolates causing foodborne illness are sent to the State Public Health Laboratories to be typed by molecular methods. The results of the typing are uploaded into a national database to detect common source outbreaks across the U.S. The typing helps to identify specific foods or food products that are the source of the infection.

Travelers' diarrhea is typically caused by toxin-producing Escherichia coli, which are the leading cause of bacterial diarrhea infections among travelers to Africa, Asia, and Latin America. These strains of E. coli, however, are different than the strains of Shiga toxin-producing E. coli (O157:H7), which can cause hemolytic uremia syndrome.

1. What can be done to prevent a bacterial infection of the digestive tract?

The best things to do are to not drink water or eat food that may be contaminated and to be careful with sanitation measures, such as hand washing. Food that might be contaminated, such as raw meats and eggs, should be cooked thoroughly. Cooked foods and foods that are served raw should not touch any surfaces that may have been contaminated. When you are traveling to developing nations, it is best to only drink bottled water, carbonated drinks, and hot cooked foods. Avoid fresh fruits and vegetables, limiting yourself to those that you can peel yourself. Food from street vendors is generally not considered safe. If someone in your household has an infection that is causing diarrhea, careful hand washing by all family members is recommended, and the person infected should not prepare food or drink for others until the infection is over.

2. Why must the stool sample be fresh?

If the stool is not fresh, or in a preservative, the proportion of the different kinds of bacteria in the stool can change no longer representing the proportions present in the gastrointestinal tract. Overgrowth of normal bacteria can sometimes prevent the detection of the pathogenic bacteria as can exposing the stool sample to temperature extremes.

3. Why shouldn't I take an over the counter anti-diarrhea medicine when I have infectious diarrhea?

Diarrhea is one of the methods your body uses to help rid itself of the infection. If you slow down or prevent this from happening by taking anti-diarrhea medication, you can prolong the amount of time that you are ill and sometimes make your infection worse.

4. Once I've had a pathogenic bacterial infection, can I be re-infected?

Generally yes. You may develop a short-term immunity against the particular strain of pathogenic bacteria that caused your infection, but there are many other types and strains of pathogenic bacteria that can make you ill if you are exposed to them.

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Article Sources

NOTE: This article is based on research that utilizes the sources cited here as well as the collective experience of the Lab Tests Online Editorial Review Board. This article is periodically reviewed by the Editorial Board and may be updated as a result of the review. Any new sources cited will be added to the list and distinguished from the original sources used.

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This article was last reviewed on October 31, 2011. | This article was last modified on March 4, 2015.

The review date indicates when the article was last reviewed from beginning to end to ensure that it reflects the most current science. A review may not require any modifications to the article, so the two dates may not always agree.

The modified date indicates that one or more changes were made to the article. Such changes may or may not result from a full review of the article, so the two dates may not always agree.